The reference level for each speaker is set to zero in order to allow you to adjust each speaker either up or down in order to make them all match. Note that this is just a relative adjustment to the volume controlled by the main volume knob. Asuming your main volume isn't cranked way up you're not going to hurt your speakers. The manual recommends using a sound pressure meter and setting each speaker so that it outputs 75 dB.

I arbitrarily start with the test tone playing on my left speaker, adjust the main volume until its at 75 dB, switch to the next speaker and either boost or cut the speaker's individual reference level until the meter reads 75 dB.